comparison downsample.xml @ 0:20823bce09e7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/downsample commit dd00e60bdbb1fb45d395bb59dd60795e39867624

0:20823bce09e7

<?xml version="1.0"?>
<tool id="dynamic_downsample" name="Dynamically downsample" version="1.0.0">
    <description>reads to desired coverage</description>
    <requirements>
        <requirement type="package" version="1.9">samtools</requirement>
        <requirement type="package" version="5.0.1">gawk</requirement>
    </requirements>
    <command><![CDATA[
        if FACTOR=\$(samtools depth '$reads' | awk '{ a[i++]=\$3; } END { x=int((i+1)/2); if (x < (i+1)/2) y=(a[x-1]+a[x])/2; else y=a[x-1]; f = 1/(y/$coverage) ; if (f >= 1) exit 1 ; else print f }') ;
            then samtools view '$reads' -s \$FACTOR -O $reads.datatype -o '$output' ;
        else ;
            cp '$reads' '$output'
        fi
        ]]>
    </command>
    <inputs>
        <param name="reads" type="data" format="sam,bam" label="Reads to downsample" />
        <param name="coverage" type="integer" value="1000" label="Target coverage" />
    </inputs>
    <outputs>
        <data format="bam" name="output" label="${tool.name} on ${on_string} (Downsampled to ${coverage}x coverage)">
            <change_format>
                <when input="reads" value="sam" format="sam" />
            </change_format>
        </data>
    </outputs>
    <tests>
    </tests>
    <help>
    </help>
    <citations>
    </citations>
</tool>